RESUMEN
BACKGROUND: Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns during 2020-2022, in a setting of changing policy. We describe sequencing efforts and genomic epidemiologic findings across LTCFs and perform in-depth analysis in a single county. METHODS: We assessed genomic data representativeness, built phylogenetic trees, and conducted discrete trait analysis to estimate introduction sizes over time, and explored selected outbreaks to further characterize transmission events. RESULTS: We found that transmission dynamics among cases associated with LTCFs in WA changed over the course of the COVID-19 pandemic, with variable introduction rates into LTCFs, but decreasing amplification within LTCFs. SARS-CoV-2 lineages circulating in LTCFs were similar to those circulating in communities at the same time. Transmission between staff and residents was bi-directional. CONCLUSIONS: Understanding transmission dynamics within and between LTCFs using genomic epidemiology on a broad scale can assist in targeting policies and prevention efforts. Tracking facility-level outbreaks can help differentiate intra-facility outbreaks from high community transmission with repeated introduction events. Based on our study findings, methods for routine tree building and overlay of epidemiologic data for hypothesis generation by public health practitioners are recommended. Discrete trait analysis added valuable insight and can be considered when representative sequencing is performed. Cluster detection tools, especially those that rely on distance thresholds, may be of more limited use given current data capture and timeliness. Importantly, we noted a decrease in data capture from LTCFs over time. Depending on goals for use of genomic data, sentinel surveillance should be increased or targeted surveillance implemented to ensure available data for analysis.
Asunto(s)
COVID-19 , Humanos , COVID-19/epidemiología , Pandemias/prevención & control , SARS-CoV-2/genética , Washingtón/epidemiología , Cuidados a Largo Plazo/métodos , Filogenia , GenómicaRESUMEN
Genomic data provides useful information for public health practice, particularly when combined with epidemiologic data. However, sampling bias is a concern because inferences from nonrandom data can be misleading. In March 2021, the Washington State Department of Health, USA, partnered with submitting and sequencing laboratories to establish sentinel surveillance for SARS-CoV-2 genomic data. We analyzed available genomic and epidemiologic data during presentinel and sentinel periods to assess representativeness and timeliness of availability. Genomic data during the presentinel period was largely unrepresentative of all COVID-19 cases. Data available during the sentinel period improved representativeness for age, death from COVID-19, outbreak association, long-term care facility-affiliated status, and geographic coverage; timeliness of data availability and captured viral diversity also improved. Hospitalized cases were underrepresented, indicating a need to increase inpatient sampling. Our analysis emphasizes the need to understand and quantify sampling bias in phylogenetic studies and continue evaluation and improvement of public health surveillance systems.
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COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/epidemiología , Washingtón/epidemiología , Vigilancia de Guardia , Filogenia , GenómicaRESUMEN
An outbreak of novel coronavirus (2019-nCoV) that began in Wuhan, China, has spread rapidly, with cases now confirmed in multiple countries. We report the first case of 2019-nCoV infection confirmed in the United States and describe the identification, diagnosis, clinical course, and management of the case, including the patient's initial mild symptoms at presentation with progression to pneumonia on day 9 of illness. This case highlights the importance of close coordination between clinicians and public health authorities at the local, state, and federal levels, as well as the need for rapid dissemination of clinical information related to the care of patients with this emerging infection.
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Betacoronavirus/genética , Infecciones por Coronavirus , Pulmón/diagnóstico por imagen , Neumonía Viral , Adulto , Betacoronavirus/aislamiento & purificación , Análisis Químico de la Sangre , COVID-19 , Prueba de COVID-19 , China , Técnicas de Laboratorio Clínico , Infecciones por Coronavirus/diagnóstico , Infecciones por Coronavirus/terapia , Infecciones por Coronavirus/transmisión , Progresión de la Enfermedad , Genoma Viral , Humanos , Pulmón/patología , Masculino , Neumonía Viral/diagnóstico , Neumonía Viral/terapia , Neumonía Viral/transmisión , Radiografía Torácica , SARS-CoV-2 , Análisis de Secuencia de ADN , Viaje , Estados UnidosRESUMEN
BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with 7 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. METHODS: Our study includes individuals with positive SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) in the Washington Disease Reporting System with available viral genome data, from 1 December 2020 to 14 January 2022. The analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for hospitalization risk following infection with a variant, adjusting for age, sex, calendar week, and vaccination. RESULTS: In total, 58 848 cases were sequenced through sentinel surveillance, of which 1705 (2.9%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.20, 95% confidence interval [CI] 2.40-4.26), Beta (HR 2.85, 95% CI 1.56-5.23), Delta (HR 2.28 95% CI 1.56-3.34), or Alpha (HR 1.64, 95% CI 1.29-2.07) compared to infections with ancestral lineages; Omicron (HR 0.92, 95% CI .56-1.52) showed no significant difference in risk. Following Alpha, Gamma, or Delta infection, unvaccinated patients show higher hospitalization risk, while vaccinated patients show no significant difference in risk, both compared to unvaccinated, ancestral lineage cases. Hospitalization risk following Omicron infection is lower with vaccination. CONCLUSIONS: Infection with Alpha, Gamma, or Delta results in a higher hospitalization risk, with vaccination attenuating that risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.
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COVID-19 , SARS-CoV-2 , COVID-19/epidemiología , Hospitalización , Humanos , Estudios Retrospectivos , SARS-CoV-2/genética , Washingtón/epidemiologíaRESUMEN
Okanogan County, Washington, experienced increased community transmission of SARS-CoV-2, the virus that causes COVID-19, during summer 2020 (1). Multiple COVID-19 outbreaks occurred in agricultural settings, including a large outbreak among employees of a fruit grower during May-August. Because of this outbreak, Okanogan County Public Health and the Washington State Department of Health initiated one-time, on-site screening testing (2) of all orchard and warehouse employees in August 2020 and assessed risk factors for SARS-CoV-2 infection. Among 3,708 known orchard employees, a valid SARS-CoV-2 test result or information on COVID-19-like symptoms in the absence of a test was available for 3,013 (81%). Cumulative incidence of SARS-CoV-2 infection during approximately 3 months among tested orchard employees was 6%. Cumulative incidence was 12% in employees residing in the community, compared with 4% in employees residing in farmworker housing (p<0.001); point prevalence during the single screening testing event was 1% in both groups. Among 1,247 known warehouse employees, a valid result was available for 726 (58%). Cumulative incidence over approximately 3 months among tested warehouse employees was 23%, with substantial variation across job roles. Positive test results were received by 28% of employees who worked packing and sorting fruit, 24% of those in other roles in the packing and sorting area, 10% of forklift operators, 7% of employees in other warehouse roles, and 6% of office employees. Point prevalence among all warehouse workers was 1% at the screening testing event. Collaboration among employers, community groups, and public health authorities can reveal risk factors and help decrease farmworkers' risk for SARS-CoV-2 infection in the community and the workplace. Creation of a COVID-19 assessment and control plan by agricultural employers, with particular focus on indoor workers whose jobs limit physical distancing, could reduce workplace transmission.
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COVID-19/epidemiología , Brotes de Enfermedades , Agricultores/estadística & datos numéricos , Enfermedades Profesionales/epidemiología , COVID-19/prevención & control , COVID-19/transmisión , Prueba de COVID-19/estadística & datos numéricos , Humanos , Incidencia , Distanciamiento Físico , Factores de Riesgo , Washingtón/epidemiologíaRESUMEN
Workplace activities involving close contact with coworkers and customers can lead to transmission of SARS-CoV-2, the virus that causes COVID-19 (1,2). Information on the approach to and effectiveness of COVID-19 workplace investigations is limited. In May 2020, Public Health - Seattle & King County (PHSKC), King County, Washington established a COVID-19 workplace surveillance and response system to enhance COVID-19 contact tracing and identify outbreaks in workplaces. During June 15-November 15, 2020, a total of 2,881 workplaces in King County reported at least one case of COVID-19. Among 1,305 (45.3%) investigated workplaces,* 524 (40.3%) met the definition of a workplace outbreak. Among 306 (58.4%) workplaces with complete data,§ an average of 4.4 employee COVID-19 cases¶ (median = three; range = 1-65) were identified per outbreak, with an average attack rate among employees of 17.5%. PHSKC and the Washington State Department of Health optimized resources by establishing a classification scheme to prioritize workplace investigations as high, medium, or low priority based on workplace features observed to be associated with increased COVID-19 spread and workforce features associated with severe disease outcomes. High-priority investigations were significantly more likely than medium- and low-priority investigations to have two or more cases among employees (p<0.001), two or more cases not previously linked to the workplace (p<0.001), or two or more exposed workplace contacts not previously identified during case interviews (p = 0.002). Prioritization of workplace investigations allowed for the allocation of limited resources to effectively conduct workplace investigations to limit the potential workplace spread of COVID-19. Workplace investigations can also serve as an opportunity to provide guidance on preventing workplace exposures to SARS-CoV-2, facilitate access to vaccines, and strengthen collaborations between public health and businesses.
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COVID-19/epidemiología , Salud Laboral , Vigilancia en Salud Pública , COVID-19/transmisión , Trazado de Contacto , Humanos , Relaciones Interprofesionales , Washingtón/epidemiología , Lugar de TrabajoRESUMEN
We describe the contact investigation for an early confirmed case of coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in the United States. Contacts of the case-patient were identified, actively monitored for symptoms, interviewed for a detailed exposure history, and tested for SARS-CoV-2 infection by real-time reverse transcription PCR (rRT-PCR) and ELISA. Fifty contacts were identified and 38 (76%) were interviewed, of whom 11 (29%) reported unprotected face-to-face interaction with the case-patient. Thirty-seven (74%) had respiratory specimens tested by rRT-PCR, and all tested negative. Twenty-three (46%) had ELISA performed on serum samples collected ≈6 weeks after exposure, and none had detectable antibodies to SARS-CoV-2. Among contacts who were tested, no secondary transmission was identified in this investigation, despite unprotected close interactions with the infectious case-patient.
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Betacoronavirus/patogenicidad , Trazado de Contacto/estadística & datos numéricos , Infecciones por Coronavirus/epidemiología , Pandemias , Neumonía Viral/epidemiología , Adolescente , Adulto , Anciano , Betacoronavirus/genética , COVID-19 , Prueba de COVID-19 , Niño , Preescolar , Técnicas de Laboratorio Clínico/métodos , Infecciones por Coronavirus/diagnóstico , Ensayo de Inmunoadsorción Enzimática , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Neumonía Viral/diagnóstico , Salud Pública/métodos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , SARS-CoV-2 , Viaje , Washingtón/epidemiologíaRESUMEN
In October 2016, Seattle Children's Hospital notified the Washington State Department of Health (DOH) and CDC of a cluster of acute onset of limb weakness in children aged ≤14 years. All patients had distinctive spinal lesions largely restricted to gray matter detected by magnetic resonance imaging (MRI), consistent with acute flaccid myelitis (AFM). On November 3, DOH issued a health advisory to local health jurisdictions requesting that health care providers report similar cases. By January 24, 2017, DOH and CDC had confirmed 10 cases of AFM and excluded two suspected cases among residents of Washington during September-November 2016. Upper respiratory tract, stool, rectal, serum, buccal, and cerebrospinal fluid (CSF) specimens were tested for multiple pathogens. Hypothesis-generating interviews were conducted with patients or their parents to determine commonalities between cases. No common etiology or source of exposure was identified. Polymerase chain reaction (PCR) testing detected enterovirus D68 (EV-D68) in nasopharyngeal swabs of two patients, one of whom also tested positive for adenovirus by PCR, and detected enterovirus A71 (EV-A71) in the stool of a third patient. Mycoplasma spp. immunoglobulin M (IgM) titer was elevated in two patients, but both had upper respiratory swabs that tested negative for Mycoplasma spp. by PCR. Clinicians should maintain vigilance for AFM and report cases as soon as possible to state or local health departments.
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Mielitis/diagnóstico , Parálisis/diagnóstico , Enfermedad Aguda , Adolescente , Niño , Preescolar , Análisis por Conglomerados , Femenino , Humanos , Masculino , Mielitis/epidemiología , Parálisis/epidemiología , Washingtón/epidemiologíaRESUMEN
During June-July 2015, Public Health-Seattle & King County (PHSKC) and Washington State Department of Health (WADOH) investigated 22 clusters of Salmonella serotype I 4,[5], 12:i:- infections. Serotype I 4,[5], 12:i:- is the fifth most frequently reported Salmonella serotype in the United States, but is uncommon in Washington. On July 29, 2015, WADOH and PHSKC requested assistance from CDC to identify the infection source, determine risk factors, and make recommendations for prevention.
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Brotes de Enfermedades , Farmacorresistencia Bacteriana Múltiple , Microbiología de Alimentos , Carne/microbiología , Intoxicación Alimentaria por Salmonella/epidemiología , Salmonella/efectos de los fármacos , Salmonella/aislamiento & purificación , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Animales , Niño , Preescolar , Femenino , Humanos , Lactante , Masculino , Persona de Mediana Edad , Porcinos , Washingtón/epidemiología , Adulto JovenRESUMEN
Groups of tuberculosis cases with indistinguishable Mycobacterium tuberculosis genotypes (clusters) might represent recent transmission. We compared geospatial concentration of genotype clusters with independent priority rankings determined by local public health officials; findings were highly correlated. Routine use of geospatial statistics could help health departments identify recent disease transmission.
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Prioridades en Salud , Tuberculosis Pulmonar/epidemiología , Análisis por Conglomerados , Interpretación Estadística de Datos , Transmisión de Enfermedad Infecciosa , Genotipo , Humanos , Mycobacterium tuberculosis/genética , Tuberculosis Pulmonar/microbiología , Tuberculosis Pulmonar/transmisión , Washingtón/epidemiologíaAsunto(s)
Enfermedades Asintomáticas/epidemiología , Brotes de Enfermedades , Vacuna contra el Sarampión-Parotiditis-Rubéola/administración & dosificación , Paperas/epidemiología , Paperas/virología , Vacunación/estadística & datos numéricos , Esparcimiento de Virus , Femenino , Humanos , Masculino , Virus de la Parotiditis/genética , Virus de la Parotiditis/aislamiento & purificación , Virus de la Parotiditis/fisiología , Estudiantes/estadística & datos numéricos , Universidades , Washingtón/epidemiologíaRESUMEN
BACKGROUND: The COVID-19 pandemic is dominated by variant viruses; the resulting impact on disease severity remains unclear. Using a retrospective cohort study, we assessed the hospitalization risk following infection with seven SARS-CoV-2 variants. METHODS: Our study includes individuals with positive SARS-CoV-2 RT-PCR in the Washington Disease Reporting System with available viral genome data, from December 1, 2020 to January 14, 2022. The analysis was restricted to cases with specimens collected through sentinel surveillance. Using a Cox proportional hazards model with mixed effects, we estimated hazard ratios (HR) for hospitalization risk following infection with a variant, adjusting for age, sex, calendar week, and vaccination. FINDINGS: 58,848 cases were sequenced through sentinel surveillance, of which 1705 (2.9%) were hospitalized due to COVID-19. Higher hospitalization risk was found for infections with Gamma (HR 3.20, 95%CI 2.40-4.26), Beta (HR 2.85, 95%CI 1.56-5.23), Delta (HR 2.28 95%CI 1.56-3.34) or Alpha (HR 1.64, 95%CI 1.29-2.07) compared to infections with ancestral lineages; Omicron (HR 0.92, 95%CI 0.56-1.52) showed no significant difference in risk. Following Alpha, Gamma, or Delta infection, unvaccinated patients show higher hospitalization risk, while vaccinated patients show no significant difference in risk, both compared to unvaccinated, ancestral lineage cases. Hospitalization risk following Omicron infection is lower with vaccination. CONCLUSION: Infection with Alpha, Gamma, or Delta results in a higher hospitalization risk, with vaccination attenuating that risk. Our findings support hospital preparedness, vaccination, and genomic surveillance. SUMMARY: Hospitalization risk following infection with SARS-CoV-2 variant remains unclear. We find a higher hospitalization risk in cases infected with Alpha, Beta, Gamma, and Delta, but not Omicron, with vaccination lowering risk. Our findings support hospital preparedness, vaccination, and genomic surveillance.
RESUMEN
In 2016/2017, Washington State experienced a mumps outbreak despite high childhood vaccination rates, with cases more frequently detected among school-aged children and members of the Marshallese community. We sequenced 166 mumps virus genomes collected in Washington and other US states, and traced mumps introductions and transmission within Washington. We uncover that mumps was introduced into Washington approximately 13 times, primarily from Arkansas, sparking multiple co-circulating transmission chains. Although age and vaccination status may have impacted transmission, our data set could not quantify their precise effects. Instead, the outbreak in Washington was overwhelmingly sustained by transmission within the Marshallese community. Our findings underscore the utility of genomic data to clarify epidemiologic factors driving transmission and pinpoint contact networks as critical for mumps transmission. These results imply that contact structures and historic disparities may leave populations at increased risk for respiratory virus disease even when a vaccine is effective and widely used.
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Brotes de Enfermedades , Virus de la Parotiditis/fisiología , Paperas/epidemiología , Adolescente , Adulto , Niño , Preescolar , Brotes de Enfermedades/estadística & datos numéricos , Genoma Viral , Humanos , Lactante , Micronesia/etnología , Persona de Mediana Edad , Paperas/transmisión , Paperas/virología , Virus de la Parotiditis/genética , Washingtón/epidemiología , Adulto JovenRESUMEN
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has gravely affected societies around the world. Outbreaks in different parts of the globe have been shaped by repeated introductions of new viral lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State (USA) to characterize how the spread of SARS-CoV-2 in Washington State in early 2020 was shaped by differences in timing of mitigation strategies across counties and by repeated introductions of viral lineages into the state. In addition, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G but not the other variant (614D) into the state. At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant affects clinical severity or patient outcomes. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.
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COVID-19 , Genoma Viral , SARS-CoV-2 , COVID-19/virología , Brotes de Enfermedades , Humanos , Filogenia , SARS-CoV-2/genética , Washingtón/epidemiologíaRESUMEN
Between July 2018 and May 2019, Corynebacterium diphtheriae was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were microbiologically identified as nontoxigenic C. diphtheriae biovar mitis. Whole-genome sequencing confirmed that all case isolates were genetically related, associated with sequence type 445 and differing by fewer than 24 single-nucleotide polymorphisms (SNPs). Compared to publicly available C. diphtheriae genomic data, these WA isolates formed a discrete cluster with SNP variation consistent with previously reported outbreaks. Virulence-related gene content variation within the highly related WA cluster isolates was also observed. These results indicated that genome characterization can readily support epidemiology of nontoxigenic C. diphtheriae.
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Infecciones por Corynebacterium/diagnóstico , Corynebacterium diphtheriae/clasificación , Polimorfismo de Nucleótido Simple , Secuenciación Completa del Genoma/métodos , Adulto , Anciano , Corynebacterium diphtheriae/genética , Corynebacterium diphtheriae/aislamiento & purificación , Brotes de Enfermedades , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Personas con Mala Vivienda , Humanos , Masculino , Persona de Mediana Edad , Filogenia , Factores de Virulencia/genética , WashingtónRESUMEN
OBJECTIVE: To evaluate species identification and rabies virus (RABV) characterization among samples from bats submitted for rabies testing in the United States and assess whether a standardized approach to specimen selection for RABV characterization could enhance detection of a sentinel event in virus dissemination among bats. SAMPLE: United States public health rabies surveillance system data collected in January 2010 through December 2015. PROCEDURES: The number of rabies-tested bats for which species was reported and the number of RABV-positive samples for which virus characterization would likely provide information regarding introduction of novel RABV variants and translocation and host-shift events were calculated. These specimens were designated as specimens of epizootiological importance (SEIs). Additionally, the estimated test load that public health laboratories could expect if all SEIs underwent RABV characterization was determined. RESULTS: Species was reported for 74,928 of 160,017 (47%) bats submitted for rabies testing. Identified SEIs were grouped in 3 subcategories, namely nonindigenous bats; bats in southern border states, Florida, Puerto Rico, and the US Virgin Islands; and bats of species that are not commonly found to be inflected with RABV. Annually, 692 (95% CI, 600 to 784) SEIs were identified, of which only 295 (95% CI, 148 to 442) underwent virus characterization. Virus characterization of all SEIs would be expected to increase public health laboratories' overall test load by 397 (95% CI, 287 to 506) samples each year. CONCLUSIONS AND CLINICAL RELEVANCE: Species identification and RABV characterization may aid detection of a sentinel event in bat RABV dissemination. With additional resources, RABV characterization of all SEIs as a standardized approach to testing could contribute to knowledge of circulating bat RABV variants.
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Quirópteros , Virus de la Rabia , Rabia/veterinaria , Animales , Florida , Puerto Rico , Estados UnidosRESUMEN
After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.
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Betacoronavirus/genética , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/transmisión , Genoma Viral , Neumonía Viral/epidemiología , Neumonía Viral/transmisión , Teorema de Bayes , COVID-19 , Humanos , Funciones de Verosimilitud , Pandemias , Filogenia , SARS-CoV-2 , Washingtón/epidemiologíaRESUMEN
The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.